Molecular Marker Assays


David M. Francis, The Ohio State University

This module lists genotyping assays currently used for DNA sequence variation (SNP markers) and DNA size variation (SSR/microsatellite markers) with hyperlinks corresponding to pages describing the technology.

Assaying Molecular Markers

Current methods used to assay molecular markers include:

  • DNA Sequence Variation / Single Nucleotide Polymorphisms (SNPs)
    • Agarose or polyacrylamide gel electrophoresis
    • Capillary Electrophoresis
      • Applied Biosystems Snapshot
      • Single-strand conformation polymorphism (SSCP)
      • Temperature gradient capillary electrophoresis
    • Ligation Assay
      • Golden Gate (Illumina BeadXpress)
    • Allele Specific Primer Extension
      • Applied Biosystems Snapshot
      • Illumina BeadXpress
      • Illumina Infinium
      • Luminex
      • Sequenome mass spectrophotometry
    • Real Time PCR
      • High resolution melting
      • Taqman
  • DNA Size Polymorphisms (SSRs/microsatellites)

Additional Resources

For a further introduction to molecular markers, see Chapter 3 (p. 45–83), Introduction to Genomics, in:

  • Liu, B. H. 1998. Statistical genomics: Linkage, mapping, and QTL analysis. CRC Press, Boca Raton, FL.

For an introduction to molecular markers, linkage mapping, QTL analysis, and marker-assisted selection written for professional plant breeders, see:

  • Collard, B.C.Y., M.Z.Z. Jaufer, J. B. Brouwer, and E.C.K. Pang. 2005. An introduction to markers, quantitative trait locus (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica 142: 169–196. (Available online at: (verified 01 Mar 2012).

For further information relevant to allele specific primer extension, see:

  • Lee, S. H., D. R. Walker, P. B. Cregan, and H. R. Boerma. 2004. Comparison of four flow cytometric SNP detection assays and their use in plant improvement. Theoretical and Applied Genetics 110: 167–174. (Available online at: (verified 01 Mar 2012).

Funding Statement

Development of this lesson was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.

Mention of specific companies is for informational purposes and is not intended for promotion.


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